Despite the character's initial and continued popularity, Joe Musashi has not been the main character in more recent Shinobi titles, only appearing as an unlockable character in the 2002's Shinobi and its follow-up Nightshade. He also appears as an unlockable character in 2011's Shinobi 3D, which starred his father Jiro.

In addition, the heroes of Shadow Dancer (1989), Shadow Dancer: The Secret of Shinobi (1990) and The Cyber Shinobi (1990) are his descendants – the son Hayate and the grandson also named Joe, while the protagonist of Shinobi 3D is his father Jiro. The original Joe Musashi stars in the English versions of the Shadow Dancer games.

When debuting in the Shinobi series, Musashi was designed with a costume that would be described by IGN as "thoroughly traditional", whereas Sega would coordinate later characters with a post-modern aesthetic.[6] His primary weapons in most games are shuriken or kunai-like throwing knives and he also has a sword named Template:Nihongo that he can charge for a powerful special attack.[7] In addition, he also possesses various ninjitsu skill techniques and jutsu spells.[8]

Outside of video games, Joe Musashi appeared in Sonic the Comic,[9] in the Shinobi-series strips "The Dark Circle", "Fear Pavilion", "The Art of War", "Way of the Warrior" and "Power of the Elements". The Shinobi series BGM compilation was released by Wave Master in 2009 as Shinobi Music Collection – Legend of Joe Musashi.[10]

The character was received and remembered so well that he has continued to be often featured in retrospective top lists even many years after he had last starred in any title. As such, he was included in many top ten lists of the best video games ninja characters, including being ranked as second by CrunchGear in 2008,[11] as fifth by Unreality in 2009,[12] as eight by ScrewAttack and second by PC World in 2010,[13][14] as fifth by machinima.com and seventh by Cheat Code Central in 2011,[15][16] and as second by WatchMojo.com in 2013.[17] Including him on their top ten list, Virgin Media called him "the quintessential video game ninja" of the early days of gaming;[18] while according to the yet another top ten list by CraveOnline, "Joe Musashi is like the Jack Bauer of ninjas".[19] He was also featured on by PLAY's 2011 list of top ten ninja characters for the PlayStation consoles, with a comment regretting his replacement for the 2002's Shinobi by "some berk called Hotsuma",[20] and ranked as the fourth swiftest ninja by Complex in 2012.[21]

In 2000, GameSpot's news editor Shahed Ahmed named Joe Musashi as his "unquestionably" favorite all-time video game character of any kind, adding that it was Musashi's "complex mix of subtle style and violent fury that was so appealing."[22] In 2004, 1UP.com ranked Musashi as the number one video game ninja ever, adding: "Hotsuma who?".[23] In 2008, GameDaily ranked him as the second top Sega character, behind only Sega's flagship character Sonic the Hedgehog.[24] In 2009, GameDaily also listed "the badass ninja" as the fifth best video game archetype, citing Musashi as its epitome.[25] Similarly, including him on the 2004 list of "top ten forces of good", Retro Gamer opined that "ninjas are just plain cool, and Shinobi (aka Joe Musashi) is by far the most impressive member of this elite group of assassins."[26] In 2012, Complex included "Capcom vs. Sega" as sixth fighting game crossover they would like to see the most, imagining Joe Musashi clashing with Capcom's Strider Hiryu.[27]

His popularity, however, appears to be fading as the time passes since his last title, especially among the new generations of gamers. In 2008, when readers of IGN voted on which of the two ninja would win in a Hero Showdown contest, Joe Musashi or Ryu Hayabusa of Tecmo's Ninja Gaiden and Dead or Alive series, Hayabusa won easily with 82% of the votes.[28] In 2010, GameSpot featured Musashi in the article discussing forgotten gaming mascots, but nevertheless calling him "one of the greatest video game ninjas of all time."[29]